PageRenderTime 15ms CodeModel.GetById 8ms app.highlight 2ms RepoModel.GetById 1ms app.codeStats 1ms

/tools/emboss_5/emboss_epestfind.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 71 lines | 54 code | 4 blank | 13 comment | 0 complexity | 4fb46aefd456a9f58c7b8a93523b4153 MD5 | raw file
 1<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
 2  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
 5  -invalid $invalid -map $map -graph png -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>Sequence</label>
 9    </param>
10    <param name="window" size="4" type="text" value="10">
11      <label>Minimal distance between positively charged amino acids</label>
12    </param>
13    <param name="order" type="select">
14      <label>Sort by</label>
15      <option value="3">Score</option>
16      <option value="1">Length</option>
17      <option value="2">Position</option>
18    </param>
19    <param name="threshold" size="4" type="text" value="5.0">
20      <label>Threshold value to discriminate weak from potential PEST motifs.</label>
21    </param>
22    <param name="potential" type="select">
23      <label>Decide whether potential PEST motifs should be printed</label>
24      <option value="yes">Yes</option>
25      <option value="no">No</option>
26    </param>
27    <param name="poor" type="select">
28      <label>Decide whether poor PEST motifs should be printed</label>
29      <option value="yes">Yes</option>
30      <option value="no">No</option>
31    </param>
32    <param name="invalid" type="select">
33      <label>Decide whether invalid PEST motifs should be printed</label>
34      <option value="no">No</option>
35      <option value="yes">Yes</option>
36    </param>
37    <param name="map" type="select">
38      <label>Decide whether PEST motifs should be mapped to sequence</label>
39      <option value="yes">Yes</option>
40      <option value="no">No</option>
41    </param>
42  </inputs>
43  <outputs>
44    <data format="png" name="ofile2" />
45    <data format="epestfind" name="ofile1" />
46  </outputs>
47<!--    <tests>
48    <test>
49      <param name="input1" value="2.fasta"/>
50      <param name="window" value="10"/>
51      <param name="order" value="3"/>
52      <param name="threshold" value="5.0"/>
53      <param name="potential" value="yes"/>
54      <param name="poor" value="yes"/>
55      <param name="invalid" value="no"/>
56      <param name="map" value="yes"/>
57      <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
58    </test>
59  </tests>  output file contains file location info  -->
60  <help>
61    You can view the original documentation here_.
62    
63    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
64
65------
66
67**Citation**
68
69If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
70  </help>
71</tool>